Is there any way to get the oncoplot with out sorting gene names based on the frequency. I have a list of genes which are sorted based on my analysis. I am wondering if there is a way to get the oncoplot  in the same of order as mentioned in the list and not based on the frequency.

Hi Seeker,

maftools on bioconductor release branch doesn't support this, however the one on GitHub has this option. Install it from GitHub and plot as you would normally;

oncoplot(maf = laml, genes = ('TP53', 'DNMT3A', 'NPM1', 'RUNX1', 'CEBPA'), keepGeneOrder = TRUE)

Let me know if this is what you wanted.

-Anand.